Pangenome Evolution in the Marine BacteriumAlteromonas

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection

(2015) Nobuto Takeuchi et al.   BMC BIOLOGY

Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus

(2015) Yujun Cui et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombinant transfer in the basic genome ofEscherichia coli

(2015) Purushottam D. Dixit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis

(2015) Florent Lassalle et al.   RESEARCH IN MICROBIOLOGY

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

Ecophysiological diversity of a novel member of the genus Alteromonas, and description of Alteromonas mediterranea sp. nov.

(2014) Elena P. Ivanova et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genomes of Alteromonas australica, a world apart

(2014) Mario López-Pérez et al.   BMC GENOMICS

Contrasting Inter- and Intraspecies Recombination Patterns in the “Harveyi Clade” Vibrio Collected over Large Spatial and Temporal Scales

(2014) Henryk Urbanczyk et al.   Genome Biology and Evolution

A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species

(2014) D. Ramasamy et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates

(2014) Leonor Sánchez-Busó et al.   NATURE GENETICS

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm

(2013) Jane Hawkey et al.   BMC GENOMICS

Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome

(2013) Carsten Kuenne et al.   BMC GENOMICS

Genomic Diversity of “Deep Ecotype” Alteromonas macleodii Isolates: Evidence for Pan-Mediterranean Clonal Frames

(2013) Mario López-Pérez et al.   Genome Biology and Evolution

Generalism and the evolution of parasite virulence

(2013) Helen C. Leggett et al.   TRENDS IN ECOLOGY & EVOLUTION

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona

(2013) Zhemin Zhou et al.   PLoS Genetics

Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

(2012) Roland Hatzenpichler   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Polyclonality of Concurrent Natural Populations of Alteromonas macleodii

(2012) Aitor Gonzaga et al.   Genome Biology and Evolution

Genome Sequence of the Thermostable-Agarase-Producing Marine Bacterium Catenovulum agarivorans YM01T, Which Reveals the Presence of a Series of Agarase-Encoding Genes

(2012) X. Shi et al.   JOURNAL OF BACTERIOLOGY

Comparative Analysis of Mobilizable Genomic Islands

(2012) A. Daccord et al.   JOURNAL OF BACTERIOLOGY

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph

(2012) Mario López-Pérez et al.   Scientific Reports

Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

(2012) Eugene V. Koonin et al.   Frontiers in Cellular and Infection Microbiology

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

Genomic evolution of Vibrio cholerae

(2010) Yong-Joon Cho et al.   CURRENT OPINION IN MICROBIOLOGY

Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences

(2010) X. Didelot et al.   GENETICS

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)

(2009) Haeyoung Jeong et al.   JOURNAL OF MOLECULAR BIOLOGY

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

A rare SAR11 fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome

(2008) Jack A Gilbert et al.   ISME Journal

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS